Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA285479 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2046723.fastq.gz | Fastqsanger.gz | |||
| SRR2046724.fastq.gz | Fastqsanger.gz | |||
| SRR2046725.fastq.gz | Fastqsanger.gz | |||
| SRR2046726.fastq.gz | Fastqsanger.gz | |||
| SRR2046727.fastq.gz | Fastqsanger.gz |
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Project description:Background: Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human TRF1 or TRF2 shelterin proteins, possess also histone-like domain which is involved in protein-protein interactions e.g., with POT1b. We set to investigate the genome-wide localization pattern of TRB1 to reveal its preferential mode of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Results: Our results demonstrate that in addition to its roles at telomeres, TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis. This preference coincides with a frequent occurrence of telobox motifs in the upstream regions of genes in this category, but is not restricted to the telobox presence. Conclusions: We conclude that TRB1, in addition to its preferential telomeric localization, shows a specific genome-wide distribution pattern suggesting its role in regulation of genes involved in biogenesis of translational machinery. TRB1 DNA-binding activity investigated in 2 biological replicates (2 immunoprecipitation approaches) with controls; with technical replicates.
2015-12-21 | E-GEOD-69431 | biostudies-arrayexpress
Project description:Background: Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human TRF1 or TRF2 shelterin proteins, possess also histone-like domain which is involved in protein-protein interactions e.g., with POT1b. We set to investigate the genome-wide localization pattern of TRB1 to reveal its preferential mode of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Results: Our results demonstrate that in addition to its roles at telomeres, TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis. This preference coincides with a frequent occurrence of telobox motifs in the upstream regions of genes in this category, but is not restricted to the telobox presence. Conclusions: We conclude that TRB1, in addition to its preferential telomeric localization, shows a specific genome-wide distribution pattern suggesting its role in regulation of genes involved in biogenesis of translational machinery.
2015-12-21 | GSE69431 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE253005 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE236267 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE237185 | GEO
Project description:TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.
2024-02-12 | GSE237158 | GEO
Project description:The transcriptional machinery involved in RNA polymerase II (Pol II) transcription during oogenesis is not well characterized. In somatic cells, the Pol II general transcription factor, TFIID, containing the TATA binding protein (TBP) and 13 TBP-associated factors, is the first to bind gene promoters to nucleate pre-initiation complex formation. During oocyte growth TBP is replaced by TBP2 and Tbp2-/- female mice are sterile. Here, we show that in oocytes TBP2 stably associates with TFIIA but does not assemble into a TFIID-type complex but stabily associates with TFIIA. we demonstrate that in female germ cells the specific TBP2-TFIIA-containing transcription machinery drives transcription from oocyte-specific core promoters, which are different from those occupied by TBP/TFIID in somatic cells.
2020-11-16 | PXD016347 | Pride
Project description:The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
| PRJNA124661 | ENA
Project description:we find METTL3 associates with polyribosomes and promotes translation. METTL3 depletion inhibits translation, and both wild-type and catalytically inactive METTL3 promote translation when tethered to the 3' untranslated region (UTR) of a reporter mRNA. Mechanistically, METTL3 enhances mRNA translation through an interaction with the translation initiation machinery. m6A seq in A549 and H1299 cells, RNA seq in METTL3 knockdown cells
2016-07-03 | E-GEOD-76367 | biostudies-arrayexpress
Project description:The telomere repeat binding factors TRB1, TRB2, and TRB3 (TRB1/2/3) in Arabidopsis thaliana not only function as components of the PEAT complex involved in histone acetylation and H2A deubiquitination but also interact with Polycomb Repressive Complex 2 (PRC2) involved in H3 lysine 27 trimethylation (H3K27me3). In this study, we demonstrate that TRB1/2/3 form two additional chromatin-associated complexes, which we term TRB1/2/3-HTH1/2/3 (TRHT) and TRB1/2/3-HISTONE-DEMETHYLASE (TRHD). The TRHT complex comprises TRB1/2/3, ICU11, and HTH1/2/3, whereas the TRHD complex is composed of TRB1/2/3, ICU11, ZDP2, JMJ14, and NAC050/052. The TRHT and TRHD (TRHT/TRHD) complexes occupy a common set of target genes and cooperate to mediate JMJ14-mediated H3K4me3 demethylation and transcriptional repression. Compared with PEAT and PRC2 target genes, which are characterized by high and low levels of H3K4me3, respectively, the TRHT/TRHD target genes exhibit low to medium levels of H3K4me3. At the whole-genome level, TRB1/2/3 repress transcription at TRHT/TRHD and PRC2 target genes, while facilitating transcription at PEAT target genes. At the TRHT/TRHD target genes, the TRHT/TRHD complexes mediate transcriptional repression through both H3K4me3 demethylation-dependent and –independent mechanisms. These findings reveal the molecular mechanisms by which how the TRHT/TRHD complexes are coordinated with the PEAT and PRC2 complex to ensure the orchestration of multiple histone modifications at the whole-genome level.
2025-09-17 | GSE287720 | GEO